update

Author: gduscher

notebooks/Imaging/D1-Diffraction_Rings.ipynb

@@ -893,7 +893,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "base",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },

notebooks/Imaging/D2-Diffraction_Spots.ipynb

@@ -12,10 +12,10 @@
 
 from .kinematic import kinematic_scattering
 from .kinematic import calculate_kikuchi, calculate_holz
-from .kinematic import get_dynamical_allowed, calculate_laue_zones, center_of_laue_circle
-from .kinematic import find_sorted_bragg_reflections, get_incident_wave_vector
-from .kinematic import get_dynamically_allowed, ring_pattern_calculation, get_reflection_families
-from .kinematic import get_allowed_reflections
+from .kinematic import calculate_laue_zones, center_of_laue_circle
+from .kinematic import get_bragg_reflections, get_incident_wave_vector
+from .kinematic import get_dynamically_activated, ring_pattern_calculation, get_reflection_families
+from .kinematic import get_allowed_reflections, get_all_reflections
 
 from .diffraction_plot import plot_diffraction_pattern, plot_ring_pattern, warp
 from .diffraction_plot import plot_saed_parameter, plot_cbed_parameter, plot_holz_parameter
@@ -28,9 +28,9 @@
            'get_metric_tensor', 'get_structure_factors', 'find_nearest_zone_axis', 
            'find_angles', 'stage_rotation_matrix', 'get_zone_rotation',  'scattering_matrix',
            'gaussian', 'get_unit_cell', 'output_verbose', 'feq', 'form_factor',
-           'kinematic_scattering', 'calculate_kikuchi', 'calculate_holz', 'get_dynamical_allowed',
-           'calculate_laue_zones', 'center_of_laue_circle', 'find_sorted_bragg_reflections',
-           'get_incident_wave_vector', 'get_dynamically_allowed', 'ring_pattern_calculation',
+           'kinematic_scattering', 'calculate_kikuchi', 'calculate_holz', 'get_dynamically_activated',
+           'calculate_laue_zones', 'center_of_laue_circle', 'get_bragg_reflections',
+           'get_incident_wave_vector', 'ring_pattern_calculation', get_all_reflections,
            'get_reflection_families', 'get_allowed_reflections',
            'plot_diffraction_pattern', 'plot_ring_pattern', 'warp',
            'plot_saed_parameter', 'plot_cbed_parameter', 'plot_holz_parameter',

notebooks/Imaging/Zuo-HOLZ-experiment.jpg

@@ -28,17 +28,20 @@
 import itertools
 
 import numpy as np
+import scipy
 import matplotlib.pylab as plt  # basic plotting
 
 import ase
 import ase.build
 
 import pyTEMlib
 from pyTEMlib.crystal_tools import electronFF
+from ..utilities import get_wavelength, get_rotation_matrix
+
 
 inputKeys = ['acceleration_voltage_V', 'zone_hkl', 'Sg_max', 'hkl_max']
 optional_input_keys = ['crystal', 'lattice_parameter_nm', 'convergence_angle_mrad',
-                      'mistilt', 'thickness', 'dynamic correction', 'dynamic correction K0']
+                       'mistilt', 'thickness', 'dynamic correction', 'dynamic correction K0']
 
 
 def read_poscar(filename):
@@ -141,7 +144,6 @@ def zuo_fig_3_18(verbose=True):
 
     return atoms
 
-get_rotation_matrix = pyTEMlib.utilities.get_rotation_matrix
 
 def zone_mistilt(zone, angles):
     """ Rotation of zone axis by mistilt
@@ -173,28 +175,11 @@ def get_metric_tensor(matrix):
 
 def vector_norm(g):
     """ Length of vector
-
     depreciated - use np.linalg.norm
     """
     return np.linalg.norm(g)
 
 
-def get_wavelength(acceleration_voltage) -> float:
-    """
-    Calculates the relativistic corrected de Broglie wavelength of an electron in Angstrom
-
-    Parameter:
-    ---------
-    acceleration_voltage: float or int
-        acceleration voltage in volt
-    Returns:
-    -------
-    wavelength: float
-        wave length in Angstrom (= meter *10**10)
-    """
-    return pyTEMlib.utilities.get_wavelength(acceleration_voltage) * 1e10
-
-
 def get_all_miller_indices(hkl_max):
     """ Get all Miller indices up to hkl_max"""
     h = np.linspace(-hkl_max, hkl_max, 2 * hkl_max + 1)  # all evaluated single Miller Indices
@@ -220,6 +205,27 @@ def get_structure_factors(atoms, g_hkl):
     return np.array(structure_factors)
 
 
+def get_inner_potential(atoms):
+    """ inner potential in Volts """
+    u_0 = 0  # in (Ang)
+    # atom form factor of zero reflection angle is the inner potential in 1/A
+    for atom in atoms:
+        u_0 += form_factor(atom.symbol, 0)
+    scattering_factor_to_volts = ((scipy.constants.h*1e10)**2
+                                  / (2 * np.pi * scipy.constants.m_e * scipy.constants.e)
+                                  / atoms.cell.volume)
+    return u_0 * scattering_factor_to_volts
+
+def ewald_sphere_center(acceleration_voltage, atoms, zone_hkl):
+    """ Ewald sphere center in 1/Angstrom """
+    wavelength = get_wavelength(acceleration_voltage, unit='Å')  # in Angstrom
+    u_0 = get_inner_potential(atoms)
+    incident_wave_vector = np.sqrt(1/wavelength**2 + u_0 )#1/Ang
+
+    center = np.dot(zone_hkl, atoms.cell.reciprocal())
+    center = center / np.linalg.norm(center) * incident_wave_vector
+    return center
+
 def find_nearest_zone_axis(tags):
     """Test all zone axis up to a maximum of hkl_max"""
 
@@ -436,6 +442,7 @@ def gaussian(xx, pp):
     s1 = pp[2] / 2.3548
     prefactor = 1.0 / np.sqrt(2 * np.pi * s1 ** 2)
     y = (pp[1] * prefactor) * np.exp(-(xx - pp[0]) ** 2 / (2 * s1 ** 2))
+    
     return y
 
 
@@ -453,28 +460,28 @@ def get_unit_cell(atoms, tags):
 def output_verbose(atoms, tags):
     """ Verbose output of experimental parameters"""
     print('Experimental Parameters:')
-    print(f"Acceleration Voltage: {tags['acceleration_voltage_V']*1000:.1f} kV")
-    print(f"Convergence Angle: {tags['convergence_angle_mrad']:.2f} mrad",
-          f" = {tags['convergence_angle_A-1']:.2f} 1/Ang")
-    print(f"Wavelength: {tags['wave_length']*1000:.3f} pm")
-    print(f"Incident Wave Vector: {tags['incident_wave_vector']*10} 1/nm in material ",
-          f"; in vacumm: {1/tags['wave_length']:.4f} 1/nm")
+    print(f"Acceleration Voltage: {tags.get('acceleration_voltage_V', 0)*1000:.1f} kV")
+    print(f"Convergence Angle: {tags.get('convergence_angle_mrad', None):.2f} mrad",
+          f" = {tags.get('convergence_angle_A-1', None):.2f} 1/Ang")
+    print(f"Wavelength: {tags.get('wave_length', 0)*1000:.3f} pm")
+    print(f"Incident Wave Vector: {tags.get('incident_wave_vector', 0)*10} 1/nm in material ",
+          f"; in vacumm: {1/tags.get('wave_length', 0):.4f} 1/nm")
     print("\n Rotation to tilt zone axis onto z-axis:")
-    print(f"Rotation alpha {np.rad2deg(tags['y-axis rotation alpha']):.1f} degree, "
-              f" beta {np.rad2deg(tags['x-axis rotation beta']):.1f} degree")
-    print(f"from zone axis {tags['zone_hkl']}")
-    print(f"Tilting {1} by {np.rad2deg(tags['mistilt_alpha']):.2f} "
-          f" in alpha and {np.rad2deg(tags['mistilt_beta']):.2f}" +
+    print(f"Rotation alpha {np.rad2deg(tags.get('y-axis rotation alpha', None)):.1f} degree, "
+              f" beta {np.rad2deg(tags.get('x-axis rotation beta', None)):.1f} degree")
+    print(f"from zone axis {tags.get('zone_hkl', None)}")
+    print(f"Tilting {1} by {np.rad2deg(tags.get('mistilt_alpha', None)):.2f} "
+          f" in alpha and {np.rad2deg(tags.get('mistilt_beta', None)):.2f}" +
           " in beta direction results in :")
-    nearest = tags['nearest_zone_axes']
+    nearest = tags.get('nearest_zone_axes', {})
     print('Next nearest zone axes are:')
-    for i in range(1, nearest['amount']):
+    for i in range(1, nearest.get('amount', 0)):
         print(f"{nearest[str(i)]['hkl']}: mistilt:",
                 f" {np.rad2deg(nearest[str(i)]['mistilt_alpha']):6.2f}, "
                 f"{np.rad2deg(nearest[str(i)]['mistilt_beta']):6.2f}")
-    print('Center of Ewald sphere ', tags['k0_vector'])
-    dif = atoms.info['diffraction']
-    print('Center or Laue circle', dif['Laue_circle'])
+    print('Center of Ewald sphere ', tags.get('k0_vector', None))
+    dif = atoms.info.get('diffraction', {})
+    print('Center or Laue circle', dif.get('Laue_circle', None))
 
 
 def make_pretty_labels(hkls, hex_label=False):

notebooks/Spectroscopy/EDS.ipynb

@@ -3,16 +3,16 @@
 part of pyTEMlib's diffraction tools subpackage
 author: Gerd Duscher, UTK
 """
-import matplotlib.pyplot as plt
 
-import scipy
 import matplotlib
+import matplotlib.pyplot as plt
 from matplotlib.collections import PatchCollection
 from matplotlib.lines import Line2D
 from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
 
 import ase
 import numpy as np
+import scipy
 import sidpy
 import skimage
 
@@ -37,7 +37,7 @@ def scattering_profiles(diff_pattern, center):
     """
     polar_projection = skimage.transform.warp_polar(diff_pattern, center=center).T
     polar_projection[polar_projection<0.] = 0.
-    
+
     out_tags={'center': center,
               'polar_projection': polar_projection,
               'radial_average': polar_projection.sum(axis=1)}
@@ -359,22 +359,25 @@ def transform(coords):
     return polar, (rads, angs)
 
 def set_center(main_dataset, center, scale=None):
+    """ Set the u and v axes of a diffraction pattern dataset to center on origin"""
     if scale is None:
         axes= main_dataset.get_image_dims(return_axis=True)
         scale = (axes[0].slope, axes[1].slope)
     if isinstance(scale, float):
         scale = (scale, scale)
-    
+
     x_axis = np.linspace(0, main_dataset.shape[0]-1, main_dataset.shape[0])-center[1]
     x_axis *= scale[0]
     y_axis = np.linspace(0, main_dataset.shape[1]-1, main_dataset.shape[1])-center[0]
     y_axis *= -scale[1]
     x = sidpy.Dimension(name='u', values=x_axis)
-    
+
     main_dataset.set_dimension(0, sidpy.Dimension(name='u', values=x_axis, units='1/nm',
-                                                  dimension_type='spatial', quantity='reciprocal distance'))
+                                                  dimension_type='spatial',
+                                                  quantity='reciprocal distance'))
     main_dataset.set_dimension(1, sidpy.Dimension(name='v', values=y_axis, units='1/nm',
-                                                  dimension_type='spatial', quantity='reciprocal distance'))
+                                                  dimension_type='spatial',
+                                                  quantity='reciprocal distance'))
 
 
 def plot_ring_pattern(atoms, diffraction_pattern=None):
@@ -420,22 +423,19 @@ def plot_ring_pattern(atoms, diffraction_pattern=None):
     profile *=  extent[1]*0.5 /profile.max()
     profile_x = np.linspace(1,len(profile),len(profile))*scale
     intensity *= extent[1]*0.25 /intensity.max()
-    
+
     tags.setdefault('label_color', 'navy')
     tags.setdefault('profile color', 'navy')
     tags.setdefault('ring color', 'red')
     tags.setdefault('label_size', 10)
     tags.setdefault('profile height', 5)
     tags.setdefault('plot_scalebar', False)
-    
-    fig = plt.figure()
-    
 
-    
-    ####
+    fig = plt.figure()
+    # ###
     # show image in background
-    ####
-    
+    # ###
+
     if diffraction_pattern is not None:
         im = plt.imshow(np.log2(1+diffraction_pattern), extent=extent, cmap='gray')
         plt.colorbar(im)
@@ -463,12 +463,12 @@ def f(axis):
         if unique[j] < len(profile)*scale:
             # plot lines
             plt.plot([unique[j],unique[j]], [0, intensity[j]],c='r')
-            arc = matplotlib.patches.Arc((0,0), unique[j]*2, unique[j]*2, 
-                            angle=90.0, 
-                            theta1=0.0, theta2=270.0, 
+            arc = matplotlib.patches.Arc((0,0), unique[j]*2, unique[j]*2,
+                            angle=90.0,
+                            theta1=0.0, theta2=270.0,
                             color='r', fill= False, alpha = 0.5)
             ax.add_artist(arc)
-        
+
     # ####
     # plot profile
     # ####
@@ -480,7 +480,6 @@ def f(axis):
         index = '{'+f'{family[i][0]:.0f} {family[i][1]:.0f} {family[i][2]:.0f}'+'}' # pretty index string
         ax.text(unique[i],-0.05, index, horizontalalignment='center',
                 verticalalignment='top', rotation = 'vertical', fontsize=8, color = 'white')
-    
     return fig